Gene expression in diseased and healthy individuals is oftentimes different and characterizable. The ability to monitor gene expression in such cases provides medical professionals with a powerful diagnostic tool. This form of diagnosis is especially important in the area of oncology, where it is thought that the overexpression of an oncogene, or the underexpression of a tumor suppressor gene, results in tumorogenesis. See Mikkelson et al. J. Cell. Biochem. 1991, 46, 3-8.
One can indirectly monitor gene expression, for example, by measuring nucleic acid (e.g., mRNA) that is the transcription product of a targeted gene. The nucleic acid is chemically or biochemically labeled with a detectable moiety and allowed to hybridize with a localized nucleic acid of known sequence sometimes, known here as a probe. The detection of a labeled nucleic acid at the probe position indicates that the targeted gene has been expressed. See International Application Publication Nos. WO 97/27317, WO 92/10588 and WO 97/10365.
The labeling of a nucleic acid is typically performed by covalently attaching a detectable group (label) to either an internal or terminal position. Scientists have reported a number of detectable nucleotide analogues that have been enzymatically incorporated into an oligo- or polynucleotide. Langer et al., for example, disclosed analogues of dUTP and UTP that contain a covalently bound biotin moiety. Proc. Natl. Acad. Sci. USA 1981, 78, 6633-6637. The analogues, shown below, possess an allylamine linker arm that is attached to the C-5 position of the pyrimidine ring at one end and a biotin moiety at the other. The dUTP and UTP analogues, wherein R is H or OH, were incorporated into a polynucleotide.

Petrie et al. disclosed a dATP analogue, 3-[5-([(N-biotinyl-6-aminocaproyl)-amino)]pentyl]-1-(2-deoxy-β-D-erythro-pentofuranosyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine-5′-triphosphate. Bioconjugate Chem. 1991, 2, 441-446. The analogue, shown below, is modified at the 3-position with a linker arm that is attached to a biotin moiety. Petrie et al. reported that the compound wherein R is biotin is incorporated into DNA by nick translation.

Prober et al. disclosed a set of four dideoxynucleotides, each containing a succinylfluorescein dye. Science 1987, 238, 336-341. The dideoxynucleotides, one of which is shown below, were enzymatically incorporated into an oligonucleotide through a template directed extension of a primer. The compounds provided for a DNA sequencing method based on gel migration.

Herrlein et al. disclosed modified nucleoside triphosphates of the four DNA bases. Helv. Chim. Acta 1994, 77, 586-596. The compounds, one of which is shown below, contain a 3′-amino group containing radioactive or fluorescent moieties. Herrlein et al. further described the use of the nucleotide analogues as DNA chain terminators.

Cech et al. disclosed 3′-amino-functionalized nucleoside triphosphates. Collect. Czech. Chem. Commun. 1996, 61, S297-S300. The compounds, one of which is shown below, contain a fluorescein attached to the 3′-position through an amino linker. Cech et al. proposed that the described functionalized nucleosides would be useful as terminators for DNA sequencing.
